mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947_CJ‑RC | 1,070,246 | 2 | . | A | 76.2% | 41.5 / 11.7 | 21 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 1,070,246 | 1 | . | G | 73.7% | 34.6 / 11.7 | 21 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 60.8% | 16.0 / 82.6 | 79 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 55.7% | 20.4 / 119.7 | 97 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,558,407 | 0 | G | T | 54.5% | 4.7 / 11.2 | 12 | intergenic (‑68/+103) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 53.5% | 31.3 / 196.0 | 142 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 3,447,286 | 0 | A | C | 52.2% | ‑2.7 / 12.2 | 25 | S18R (AGC→CGC) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 4,809,883 | 0 | A | C | 50.0% | ‑6.5 / 10.5 | 8 | intergenic (‑289/‑266) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| * | NC_002947_CJ‑RC | 117,276 | 0 | C | G | 37.7% | 57.8 / 20.0 | 53 | intergenic (+56/+38) | PP_0111/metQ | electron transport protein SCO1/SenC/methionine ABC transporter substrate‑binding protein |
| * | NC_002947_CJ‑RC | 1,013,255 | 0 | A | T | 30.0% | 32.1 / 12.8 | 20 | intergenic (+83/+48) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 1,728,822 | 0 | A | C | 30.0% | 94.6 / 12.8 | 60 | G95G (GGT→GGG) | PP_1523 | hypothetical protein |
| * | NC_002947_CJ‑RC | 1,013,249 | 0 | T | G | 28.6% | 39.6 / 13.4 | 21 | intergenic (+77/+54) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 1,013,235 | 0 | A | T | 24.1% | 57.8 / 14.2 | 29 | intergenic (+63/+68) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 1,013,234 | 0 | C | A | 22.6% | 81.5 / 14.9 | 31 | intergenic (+62/+69) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 1,013,248 | 0 | A | T | 21.4% | 63.1 / 11.8 | 28 | intergenic (+76/+55) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 1,013,241 | 0 | G | C | 20.7% | 72.4 / 14.6 | 29 | intergenic (+69/+62) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 1,013,242 | 0 | G | C | 20.7% | 76.9 / 14.9 | 29 | intergenic (+70/+61) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| Marginal new junction evidence (lowest skew 10 of 13 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 35 (0.560) | 11 (0.180) | 11/280 | 5.3 | 25.6% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 30 (0.500) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 0 (0.000) | 10 (0.160) +GCC |
10/284 | 5.7 | 100% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 0 (0.000) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 2472115 | 27 (0.430) | 7 (0.120) | 7/276 | 6.8 | 13.6% | intergenic (+19/+130) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase |
| ? | NC_002947_CJ‑RC | 2472313 = | 63 (1.060) | coding (1783/1851 nt) | PP_2167 | PhoD‑like phosphatase | |||||
| * | ? | NC_002947_CJ‑RC | = 5873104 | 25 (0.400) | 4 (0.080) | 4/232 | 7.3 | 18.2% | intergenic (+50/+84) | PP_5144/ptsP | hypothetical protein/phosphoenolpyruvate‑dependent regulator |
| ? | NC_002947_CJ‑RC | = 5873139 | 16 (0.320) | intergenic (+85/+49) | PP_5144/ptsP | hypothetical protein/phosphoenolpyruvate‑dependent regulator | |||||
| * | ? | NC_002947_CJ‑RC | = 4150041 | 15 (0.240) | 5 (0.090) | 5/254 | 7.3 | 33.2% | intergenic (+40/‑357) | PP_3654/PP_3655 | leucine‑responsive regulatory protein/cytosine/purine/uracil/thiamine/allantoin permease family protein |
| ? | NC_002947_CJ‑RC | = 4150072 | 7 (0.130) | intergenic (+71/‑326) | PP_3654/PP_3655 | leucine‑responsive regulatory protein/cytosine/purine/uracil/thiamine/allantoin permease family protein | |||||
| * | ? | NC_002947_CJ‑RC | 4586141 = | 18 (0.290) | 4 (0.080) | 4/246 | 7.7 | 24.1% | intergenic (+117/+98) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947_CJ‑RC | 4586212 = | 10 (0.190) | intergenic (+188/+27) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947_CJ‑RC | = 5861679 | 19 (0.300) | 3 (0.060) | 3/230 | 7.9 | 14.3% | intergenic (+42/+96) | PP_5134/PP_5135 | hypothetical protein/ABC transporter substrate‑binding protein |
| ? | NC_002947_CJ‑RC | = 5861724 | 21 (0.420) | intergenic (+87/+51) | PP_5134/PP_5135 | hypothetical protein/ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947_CJ‑RC | = 1487035 | 27 (0.430) | 3 (0.060) | 3/230 | 7.9 | 13.2% | intergenic (+51/+79) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS |
| ? | NC_002947_CJ‑RC | = 1487065 | 18 (0.360) | intergenic (+81/+49) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS | |||||
| * | ? | NC_002947_CJ‑RC | = 5290102 | 42 (0.670) | 4 (0.070) | 4/272 | 8.3 | 5.1% | intergenic (‑80/+104) | PP_4660/mdaB | LysR family transcriptional regulator/drug activity modulator B |
| ? | NC_002947_CJ‑RC | 5290245 = | 108 (1.840) | coding (633/672 nt) | mdaB | drug activity modulator B | |||||
| * | ? | NC_002947_CJ‑RC | = 3968879 | NA (NA) | 4 (0.070) | 4/276 | 8.4 | 8.9% | coding (1007/1179 nt) | PP_3498 | transposase |
| ? | NC_002947_CJ‑RC | 3968942 = | 43 (0.690) | coding (1070/1179 nt) | PP_3498 | transposase | |||||